Kate Culhane, Dept. of Ecology, Evolution, and Marine Biology, UC Santa Barbara
kathrynculhane@ucsb.edu


SUMMARY

Exploring the data


DEPENDENCIES

##### PACKAGES #####

library(tidyverse) # data manipulation & visualization
library(vegan) # community analyses
library(goeveg) # scree plot for NMDS

##### DATA #####

# Invertebrate counts by order from sticky and pitfall trap samples
prey <- read_csv("output/02_prey.csv")

# Invertebrate counts by order from lizard stomach pumping samples
diet <- read_csv("output/02_diet_inverts.csv")

# Site by species matrix (invert prey data)
prey_matrix <- read_csv("output/02_prey_matrix.csv")

# Site by species matrix (diet data)
diet_matrix <- read_csv("output/02_diet_matrix.csv")

Abundance by order

Available prey community

# Summary table
prey %>% 
  group_by(order, trap_type) %>% 
  summarise(n = sum(count)) %>% 
  pivot_wider(names_from = trap_type, values_from = n) %>% 
  mutate(total = pitfall + sticky) %>% 
  arrange(-total)
# Abundance by order
prey %>% 
  ggplot(aes(x = trap_type, y = count)) +
  geom_jitter(aes(color = trap_type),
              width = 0.1, size = 1.5) +
  geom_boxplot(fill = NA, outlier.shape = NA) +
  facet_wrap(~ fct_reorder(order, count, .fun = sum, .desc = TRUE),
             scales = "free_y") +
  theme_classic() +
  theme(legend.position = "NA") +
  labs(x = "Trap type", y = "Abundance (indv/trap)")

Diet

# Summary table
diet %>% 
  group_by(order) %>% 
  summarise(n = sum(count)) %>% 
  arrange(-n)
# Abundance by order
diet %>% 
  # Data wrangling
  group_by(order) %>% 
  mutate(n = length(count)) %>% 
  # Plot
  ggplot(aes(x = fct_reorder(order, count, .fun = sum, .desc = TRUE), y = count)) +
  geom_jitter(width = 0.1, size = 1.5) +
  geom_boxplot(fill = NA, outlier.shape = NA) +
  geom_text(aes(y = 80, label = paste("n =", n)),
            stat = "unique", angle = 90, size = 3) +
  scale_y_log10() +
  theme_classic() +
  theme(legend.position = "NA",
        axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1)) +
  labs(x = "Order", y = "Abundance (indv/lizard)")

NMDS

Invert trap data

# Wrangle matrix
m_p <- as.matrix(prey_matrix[-c(1:4)])
rownames(m_p) <- prey_matrix$sample
m_p_hell <- decostand(m_p, 'hellinger') # Hellinger transformation
m_p_meta <- select(prey_matrix, sample, site, trap, trap_type) # metadata

# Scree plot to check stress per number of dimensions
dimcheckMDS(m_p_hell, distance = "bray", autotransform = FALSE, k = 10)

## Run 0 stress 0.2455473 
## Run 1 stress 0.473834 
## Run 2 stress 0.4723164 
## Run 3 stress 0.2228119 
## ... New best solution
## ... Procrustes: rmse 0.01731212  max resid 0.1986803 
## Run 4 stress 0.4719769 
## Run 5 stress 0.223215 
## ... Procrustes: rmse 0.004923924  max resid 0.06419877 
## Run 6 stress 0.4720854 
## Run 7 stress 0.2228233 
## ... Procrustes: rmse 0.0005059689  max resid 0.004540309 
## ... Similar to previous best
## Run 8 stress 0.465649 
## Run 9 stress 0.2298373 
## Run 10 stress 0.2287735 
## Run 11 stress 0.2232264 
## ... Procrustes: rmse 0.004631167  max resid 0.06102247 
## Run 12 stress 0.474459 
## Run 13 stress 0.4730141 
## Run 14 stress 0.2228789 
## ... Procrustes: rmse 0.001190156  max resid 0.01459893 
## Run 15 stress 0.2230326 
## ... Procrustes: rmse 0.00438998  max resid 0.06209094 
## Run 16 stress 0.2358193 
## Run 17 stress 0.224727 
## Run 18 stress 0.2230406 
## ... Procrustes: rmse 0.004531546  max resid 0.06418904 
## Run 19 stress 0.2287462 
## Run 20 stress 0.2357839 
## *** Solution reached
## Run 0 stress 0.1436293 
## Run 1 stress 0.147051 
## Run 2 stress 0.1479869 
## Run 3 stress 0.1542941 
## Run 4 stress 0.157293 
## Run 5 stress 0.1580501 
## Run 6 stress 0.1571429 
## Run 7 stress 0.1568249 
## Run 8 stress 0.1484989 
## Run 9 stress 0.1484684 
## Run 10 stress 0.1572966 
## Run 11 stress 0.1512325 
## Run 12 stress 0.1586262 
## Run 13 stress 0.14585 
## Run 14 stress 0.1489052 
## Run 15 stress 0.1537238 
## Run 16 stress 0.1479076 
## Run 17 stress 0.1628468 
## Run 18 stress 0.1474388 
## Run 19 stress 0.1494413 
## Run 20 stress 0.152329 
## *** No convergence -- monoMDS stopping criteria:
##      1: no. of iterations >= maxit
##     18: stress ratio > sratmax
##      1: scale factor of the gradient < sfgrmin
## Run 0 stress 0.09709427 
## Run 1 stress 0.0975036 
## ... Procrustes: rmse 0.009769245  max resid 0.1255632 
## Run 2 stress 0.09747799 
## ... Procrustes: rmse 0.009391054  max resid 0.1240968 
## Run 3 stress 0.09919853 
## Run 4 stress 0.09755056 
## ... Procrustes: rmse 0.01008272  max resid 0.09690611 
## Run 5 stress 0.09990082 
## Run 6 stress 0.09762724 
## Run 7 stress 0.09735131 
## ... Procrustes: rmse 0.009532866  max resid 0.0972117 
## Run 8 stress 0.09709445 
## ... Procrustes: rmse 0.0002246076  max resid 0.002686827 
## ... Similar to previous best
## Run 9 stress 0.09744186 
## ... Procrustes: rmse 0.009436546  max resid 0.09221591 
## Run 10 stress 0.09735411 
## ... Procrustes: rmse 0.009369763  max resid 0.09688807 
## Run 11 stress 0.1003504 
## Run 12 stress 0.09764309 
## Run 13 stress 0.0997154 
## Run 14 stress 0.09994785 
## Run 15 stress 0.09771122 
## Run 16 stress 0.09706002 
## ... New best solution
## ... Procrustes: rmse 0.002954216  max resid 0.03998377 
## Run 17 stress 0.09768524 
## Run 18 stress 0.09765987 
## Run 19 stress 0.0970586 
## ... New best solution
## ... Procrustes: rmse 0.0004263772  max resid 0.00418592 
## ... Similar to previous best
## Run 20 stress 0.09730263 
## ... Procrustes: rmse 0.004970963  max resid 0.0572948 
## *** Solution reached
## Run 0 stress 0.07047178 
## Run 1 stress 0.07176096 
## Run 2 stress 0.07029202 
## ... New best solution
## ... Procrustes: rmse 0.007438677  max resid 0.06143557 
## Run 3 stress 0.07025245 
## ... New best solution
## ... Procrustes: rmse 0.003279147  max resid 0.02997311 
## Run 4 stress 0.07104961 
## Run 5 stress 0.07046098 
## ... Procrustes: rmse 0.005122288  max resid 0.04941762 
## Run 6 stress 0.07103114 
## Run 7 stress 0.07102986 
## Run 8 stress 0.07038575 
## ... Procrustes: rmse 0.004627424  max resid 0.06317074 
## Run 9 stress 0.07025476 
## ... Procrustes: rmse 0.001174339  max resid 0.01537297 
## Run 10 stress 0.07110796 
## Run 11 stress 0.07153529 
## Run 12 stress 0.07108121 
## Run 13 stress 0.07115929 
## Run 14 stress 0.07027192 
## ... Procrustes: rmse 0.002205914  max resid 0.02496444 
## Run 15 stress 0.07113186 
## Run 16 stress 0.0711633 
## Run 17 stress 0.07025549 
## ... Procrustes: rmse 0.001357963  max resid 0.01274137 
## Run 18 stress 0.07113844 
## Run 19 stress 0.0702544 
## ... Procrustes: rmse 0.0003403458  max resid 0.004119722 
## ... Similar to previous best
## Run 20 stress 0.07110164 
## *** Solution reached
## Run 0 stress 0.05433226 
## Run 1 stress 0.05435536 
## ... Procrustes: rmse 0.002197148  max resid 0.01414371 
## Run 2 stress 0.05446114 
## ... Procrustes: rmse 0.008052334  max resid 0.08931407 
## Run 3 stress 0.05439223 
## ... Procrustes: rmse 0.005707055  max resid 0.07053331 
## Run 4 stress 0.05460937 
## ... Procrustes: rmse 0.01631002  max resid 0.0819997 
## Run 5 stress 0.05448055 
## ... Procrustes: rmse 0.005422432  max resid 0.05878164 
## Run 6 stress 0.05438171 
## ... Procrustes: rmse 0.004596542  max resid 0.05899845 
## Run 7 stress 0.05440612 
## ... Procrustes: rmse 0.009614012  max resid 0.08976012 
## Run 8 stress 0.05442542 
## ... Procrustes: rmse 0.00844972  max resid 0.08237777 
## Run 9 stress 0.05448582 
## ... Procrustes: rmse 0.01591553  max resid 0.08040107 
## Run 10 stress 0.05448977 
## ... Procrustes: rmse 0.01623271  max resid 0.08167314 
## Run 11 stress 0.0544841 
## ... Procrustes: rmse 0.00540828  max resid 0.05272724 
## Run 12 stress 0.05458539 
## ... Procrustes: rmse 0.01177617  max resid 0.09362556 
## Run 13 stress 0.05439498 
## ... Procrustes: rmse 0.004333892  max resid 0.05062166 
## Run 14 stress 0.05438809 
## ... Procrustes: rmse 0.006448776  max resid 0.0876939 
## Run 15 stress 0.05437136 
## ... Procrustes: rmse 0.004723722  max resid 0.06611154 
## Run 16 stress 0.0546297 
## ... Procrustes: rmse 0.0166029  max resid 0.0820563 
## Run 17 stress 0.05446684 
## ... Procrustes: rmse 0.006189069  max resid 0.05984547 
## Run 18 stress 0.05504664 
## Run 19 stress 0.05433407 
## ... Procrustes: rmse 0.0008277278  max resid 0.004330551 
## ... Similar to previous best
## Run 20 stress 0.0543633 
## ... Procrustes: rmse 0.005573439  max resid 0.07822644 
## *** Solution reached
## Run 0 stress 0.04561447 
## Run 1 stress 0.04576188 
## ... Procrustes: rmse 0.008535841  max resid 0.08782132 
## Run 2 stress 0.04656548 
## Run 3 stress 0.04706558 
## Run 4 stress 0.04687136 
## Run 5 stress 0.04563521 
## ... Procrustes: rmse 0.006278656  max resid 0.08607648 
## Run 6 stress 0.04583243 
## ... Procrustes: rmse 0.0109735  max resid 0.08013107 
## Run 7 stress 0.04600532 
## ... Procrustes: rmse 0.009715914  max resid 0.05178756 
## Run 8 stress 0.0456371 
## ... Procrustes: rmse 0.002504273  max resid 0.02549081 
## Run 9 stress 0.04585001 
## ... Procrustes: rmse 0.01212621  max resid 0.08465542 
## Run 10 stress 0.04578779 
## ... Procrustes: rmse 0.01450285  max resid 0.09880397 
## Run 11 stress 0.04618146 
## Run 12 stress 0.04571355 
## ... Procrustes: rmse 0.01091735  max resid 0.09952246 
## Run 13 stress 0.04557393 
## ... New best solution
## ... Procrustes: rmse 0.007472039  max resid 0.09869587 
## Run 14 stress 0.04560337 
## ... Procrustes: rmse 0.007219815  max resid 0.09783747 
## Run 15 stress 0.04648267 
## Run 16 stress 0.04633689 
## Run 17 stress 0.04615614 
## Run 18 stress 0.04661499 
## Run 19 stress 0.04633442 
## Run 20 stress 0.04678188 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
## Run 0 stress 0.03951312 
## Run 1 stress 0.040215 
## Run 2 stress 0.04003901 
## Run 3 stress 0.04008733 
## Run 4 stress 0.04016194 
## Run 5 stress 0.04001916 
## Run 6 stress 0.03967042 
## ... Procrustes: rmse 0.002769614  max resid 0.02839586 
## Run 7 stress 0.04065189 
## Run 8 stress 0.04092821 
## Run 9 stress 0.04097991 
## Run 10 stress 0.04107712 
## Run 11 stress 0.03981163 
## ... Procrustes: rmse 0.009263066  max resid 0.05685012 
## Run 12 stress 0.04003494 
## Run 13 stress 0.03961997 
## ... Procrustes: rmse 0.004381001  max resid 0.03751196 
## Run 14 stress 0.04099444 
## Run 15 stress 0.04053131 
## Run 16 stress 0.04048298 
## Run 17 stress 0.04047862 
## Run 18 stress 0.04043364 
## Run 19 stress 0.04053737 
## Run 20 stress 0.03991251 
## ... Procrustes: rmse 0.009682115  max resid 0.1020571 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
## Run 0 stress 0.03474612 
## Run 1 stress 0.03493355 
## ... Procrustes: rmse 0.008277399  max resid 0.1037568 
## Run 2 stress 0.03579384 
## Run 3 stress 0.03539244 
## Run 4 stress 0.03567962 
## Run 5 stress 0.03563182 
## Run 6 stress 0.03542742 
## Run 7 stress 0.03488527 
## ... Procrustes: rmse 0.01352326  max resid 0.1058673 
## Run 8 stress 0.03506371 
## ... Procrustes: rmse 0.009217526  max resid 0.1031214 
## Run 9 stress 0.03551687 
## Run 10 stress 0.03595592 
## Run 11 stress 0.03499921 
## ... Procrustes: rmse 0.005386445  max resid 0.03285242 
## Run 12 stress 0.03483764 
## ... Procrustes: rmse 0.005669398  max resid 0.04360363 
## Run 13 stress 0.03505158 
## ... Procrustes: rmse 0.01298077  max resid 0.06586003 
## Run 14 stress 0.03566764 
## Run 15 stress 0.03493322 
## ... Procrustes: rmse 0.008508611  max resid 0.09777426 
## Run 16 stress 0.03542118 
## Run 17 stress 0.03563835 
## Run 18 stress 0.03497099 
## ... Procrustes: rmse 0.01098578  max resid 0.09918192 
## Run 19 stress 0.03518141 
## ... Procrustes: rmse 0.01466542  max resid 0.09990068 
## Run 20 stress 0.03509173 
## ... Procrustes: rmse 0.009807319  max resid 0.1045895 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
## Run 0 stress 0.03098824 
## Run 1 stress 0.03166019 
## Run 2 stress 0.03189484 
## Run 3 stress 0.03156419 
## Run 4 stress 0.03164194 
## Run 5 stress 0.03202007 
## Run 6 stress 0.03192216 
## Run 7 stress 0.03125804 
## ... Procrustes: rmse 0.01267131  max resid 0.05966812 
## Run 8 stress 0.03156993 
## Run 9 stress 0.03161224 
## Run 10 stress 0.03191758 
## Run 11 stress 0.0315357 
## Run 12 stress 0.03153151 
## Run 13 stress 0.03133851 
## ... Procrustes: rmse 0.01415195  max resid 0.1011115 
## Run 14 stress 0.03197711 
## Run 15 stress 0.03149894 
## Run 16 stress 0.0316026 
## Run 17 stress 0.03130238 
## ... Procrustes: rmse 0.01106221  max resid 0.05656353 
## Run 18 stress 0.03152832 
## Run 19 stress 0.03159372 
## Run 20 stress 0.03115157 
## ... Procrustes: rmse 0.006513012  max resid 0.03358866 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
## Run 0 stress 0.02752796 
## Run 1 stress 0.02819517 
## Run 2 stress 0.02836264 
## Run 3 stress 0.02814889 
## Run 4 stress 0.02816129 
## Run 5 stress 0.02824675 
## Run 6 stress 0.02880824 
## Run 7 stress 0.02805976 
## Run 8 stress 0.02780216 
## ... Procrustes: rmse 0.005694316  max resid 0.03513871 
## Run 9 stress 0.0279111 
## ... Procrustes: rmse 0.0143536  max resid 0.0841367 
## Run 10 stress 0.0281309 
## Run 11 stress 0.0278135 
## ... Procrustes: rmse 0.01066425  max resid 0.07802394 
## Run 12 stress 0.02809477 
## Run 13 stress 0.02789513 
## ... Procrustes: rmse 0.01640333  max resid 0.08038254 
## Run 14 stress 0.02811373 
## Run 15 stress 0.02798192 
## ... Procrustes: rmse 0.01159462  max resid 0.08616648 
## Run 16 stress 0.02817648 
## Run 17 stress 0.02826769 
## Run 18 stress 0.02854547 
## Run 19 stress 0.02829301 
## Run 20 stress 0.02825553 
## *** No convergence -- monoMDS stopping criteria:
##     20: no. of iterations >= maxit
##  [1] 0.22281194 0.14362935 0.09705860 0.07025245 0.05433226 0.04557393 0.03951312 0.03474612 0.03098824
## [10] 0.02752796
# Create NMDS ordination
ord <- metaMDS(m_p_hell,
               distance = 'bray', # use Bray-Curtis distances
               autotransform = FALSE, # already manually transformed the matrix
               k = 3, # number of dimensions
               trymax = 1000)

# Stress plot
stressplot(ord)

# Plot ordination
scale_trap <- c("red", "orange")
names(scale_trap) <- c("pitfall", "sticky")
par(mar = c(4,4,1,1))
plot(ord, display = 'species', type = 'n')
points(ord, display = 'sites', pch = 19, col = scale_trap[m_p_meta$trap_type])
ordiellipse(ord, groups = m_p_meta$trap_type,
            label = TRUE, col = scale_trap, lwd = 2)
text(ord, display = 'species')

K = 3; ordination stress = 0.0970586

Notes & resources




Session info
devtools::session_info()
## - Session info ------------------------------------------------------------------------------------------------
##  setting  value                       
##  version  R version 4.1.0 (2021-05-18)
##  os       Windows 10 x64              
##  system   i386, mingw32               
##  ui       RStudio                     
##  language (EN)                        
##  collate  English_United States.1252  
##  ctype    English_United States.1252  
##  tz       America/Los_Angeles         
##  date     2021-07-27                  
## 
## - Packages ----------------------------------------------------------------------------------------------------
##  ! package     * version date       lib source                                 
##  P assertthat    0.2.1   2019-03-21 [?] CRAN (R 4.1.0)                         
##  P backports     1.2.1   2020-12-09 [?] CRAN (R 4.1.0)                         
##  P broom         0.7.8   2021-06-24 [?] CRAN (R 4.1.0)                         
##  P cachem        1.0.5   2021-05-15 [?] CRAN (R 4.1.0)                         
##  P callr         3.7.0   2021-04-20 [?] CRAN (R 4.1.0)                         
##  P cellranger    1.1.0   2016-07-27 [?] CRAN (R 4.1.0)                         
##  P cli           3.0.0   2021-06-30 [?] CRAN (R 4.1.0)                         
##  P cluster       2.1.2   2021-04-17 [?] CRAN (R 4.1.0)                         
##  P codetools     0.2-18  2020-11-04 [?] CRAN (R 4.1.0)                         
##  P colorspace    2.0-2   2021-06-24 [?] CRAN (R 4.1.0)                         
##  P crayon        1.4.1   2021-02-08 [?] CRAN (R 4.1.0)                         
##  P curl          4.3.2   2021-06-23 [?] CRAN (R 4.1.0)                         
##  P DBI           1.1.1   2021-01-15 [?] CRAN (R 4.1.0)                         
##  P dbplyr        2.1.1   2021-04-06 [?] CRAN (R 4.1.0)                         
##  P desc          1.3.0   2021-03-05 [?] CRAN (R 4.1.0)                         
##  P devtools      2.4.2   2021-06-07 [?] CRAN (R 4.1.0)                         
##  P digest        0.6.27  2020-10-24 [?] CRAN (R 4.1.0)                         
##  P dotCall64     1.0-1   2021-02-11 [?] CRAN (R 4.1.0)                         
##  P dplyr       * 1.0.7   2021-06-18 [?] CRAN (R 4.1.0)                         
##  P ellipsis      0.3.2   2021-04-29 [?] CRAN (R 4.1.0)                         
##  P evaluate      0.14    2019-05-28 [?] CRAN (R 4.1.0)                         
##  P fansi         0.5.0   2021-05-25 [?] CRAN (R 4.1.0)                         
##  P farver        2.1.0   2021-02-28 [?] CRAN (R 4.1.0)                         
##  P fastmap       1.1.0   2021-01-25 [?] CRAN (R 4.1.0)                         
##  P fields        12.5    2021-06-25 [?] CRAN (R 4.1.0)                         
##  P forcats     * 0.5.1   2021-01-27 [?] CRAN (R 4.1.0)                         
##  P fs            1.5.0   2020-07-31 [?] CRAN (R 4.1.0)                         
##  P generics      0.1.0   2020-10-31 [?] CRAN (R 4.1.0)                         
##  P ggplot2     * 3.3.5   2021-06-25 [?] CRAN (R 4.1.0)                         
##  P glue          1.4.2   2020-08-27 [?] CRAN (R 4.1.0)                         
##  P goeveg      * 0.5.1   2021-05-10 [?] CRAN (R 4.1.0)                         
##  P gridExtra     2.3     2017-09-09 [?] CRAN (R 4.1.0)                         
##  P gtable        0.3.0   2019-03-25 [?] CRAN (R 4.1.0)                         
##  P haven         2.4.1   2021-04-23 [?] CRAN (R 4.1.0)                         
##  P highr         0.9     2021-04-16 [?] CRAN (R 4.1.0)                         
##  P hms           1.1.0   2021-05-17 [?] CRAN (R 4.1.0)                         
##  P htmltools     0.5.1.1 2021-01-22 [?] CRAN (R 4.1.0)                         
##  P httr          1.4.2   2020-07-20 [?] CRAN (R 4.1.0)                         
##  P jsonlite      1.7.2   2020-12-09 [?] CRAN (R 4.1.0)                         
##    katereR     * 0.1.0   2021-07-28 [1] Github (katekathrynkat/katereR@4a3977e)
##  P knitr         1.33    2021-04-24 [?] CRAN (R 4.1.0)                         
##  P labeling      0.4.2   2020-10-20 [?] CRAN (R 4.1.0)                         
##  P lattice     * 0.20-44 2021-05-02 [?] CRAN (R 4.1.0)                         
##  P lifecycle     1.0.0   2021-02-15 [?] CRAN (R 4.1.0)                         
##  P lubridate   * 1.7.10  2021-02-26 [?] CRAN (R 4.1.0)                         
##  P magrittr      2.0.1   2020-11-17 [?] CRAN (R 4.1.0)                         
##  P maps          3.3.0   2018-04-03 [?] CRAN (R 4.1.0)                         
##  P MASS          7.3-54  2021-05-03 [?] CRAN (R 4.1.0)                         
##  P Matrix        1.3-3   2021-05-04 [?] CRAN (R 4.1.0)                         
##  P memoise       2.0.0   2021-01-26 [?] CRAN (R 4.1.0)                         
##  P mgcv          1.8-35  2021-04-18 [?] CRAN (R 4.1.0)                         
##  P modelr        0.1.8   2020-05-19 [?] CRAN (R 4.1.0)                         
##  P munsell       0.5.0   2018-06-12 [?] CRAN (R 4.1.0)                         
##  P nlme          3.1-152 2021-02-04 [?] CRAN (R 4.1.0)                         
##  P permute     * 0.9-5   2019-03-12 [?] CRAN (R 4.1.0)                         
##  P pillar        1.6.1   2021-05-16 [?] CRAN (R 4.1.0)                         
##  P pkgbuild      1.2.0   2020-12-15 [?] CRAN (R 4.1.0)                         
##  P pkgconfig     2.0.3   2019-09-22 [?] CRAN (R 4.1.0)                         
##  P pkgload       1.2.1   2021-04-06 [?] CRAN (R 4.1.0)                         
##  P prettyunits   1.1.1   2020-01-24 [?] CRAN (R 4.1.0)                         
##  P processx      3.5.2   2021-04-30 [?] CRAN (R 4.1.0)                         
##  P ps            1.6.0   2021-02-28 [?] CRAN (R 4.1.0)                         
##  P purrr       * 0.3.4   2020-04-17 [?] CRAN (R 4.1.0)                         
##  P R6            2.5.0   2020-10-28 [?] CRAN (R 4.1.0)                         
##  P Rcpp          1.0.6   2021-01-15 [?] CRAN (R 4.1.0)                         
##  P readr       * 1.4.0   2020-10-05 [?] CRAN (R 4.1.0)                         
##  P readxl        1.3.1   2019-03-13 [?] CRAN (R 4.1.0)                         
##  P remotes       2.4.0   2021-06-02 [?] CRAN (R 4.1.0)                         
##    renv          0.13.2  2021-03-30 [1] CRAN (R 4.1.0)                         
##  P reprex        2.0.0   2021-04-02 [?] CRAN (R 4.1.0)                         
##  P rlang         0.4.11  2021-04-30 [?] CRAN (R 4.1.0)                         
##  P rmarkdown     2.9     2021-06-15 [?] CRAN (R 4.1.0)                         
##  P rprojroot     2.0.2   2020-11-15 [?] CRAN (R 4.1.0)                         
##  P rstudioapi    0.13    2020-11-12 [?] CRAN (R 4.1.0)                         
##  P rvest         1.0.0   2021-03-09 [?] CRAN (R 4.1.0)                         
##  P scales        1.1.1   2020-05-11 [?] CRAN (R 4.1.0)                         
##  P sessioninfo   1.1.1   2018-11-05 [?] CRAN (R 4.1.0)                         
##  P spam          2.7-0   2021-06-25 [?] CRAN (R 4.1.0)                         
##  P stringi       1.6.2   2021-05-17 [?] CRAN (R 4.1.0)                         
##  P stringr     * 1.4.0   2019-02-10 [?] CRAN (R 4.1.0)                         
##  P testthat      3.0.4   2021-07-01 [?] CRAN (R 4.1.0)                         
##  P tibble      * 3.1.2   2021-05-16 [?] CRAN (R 4.1.0)                         
##  P tidyr       * 1.1.3   2021-03-03 [?] CRAN (R 4.1.0)                         
##  P tidyselect    1.1.1   2021-04-30 [?] CRAN (R 4.1.0)                         
##  P tidyverse   * 1.3.1   2021-04-15 [?] CRAN (R 4.1.0)                         
##  P usethis       2.0.1   2021-02-10 [?] CRAN (R 4.1.0)                         
##  P utf8          1.2.1   2021-03-12 [?] CRAN (R 4.1.0)                         
##  P vctrs         0.3.8   2021-04-29 [?] CRAN (R 4.1.0)                         
##  P vegan       * 2.5-7   2020-11-28 [?] CRAN (R 4.1.0)                         
##  P viridis       0.6.1   2021-05-11 [?] CRAN (R 4.1.0)                         
##  P viridisLite   0.4.0   2021-04-13 [?] CRAN (R 4.1.0)                         
##  P withr         2.4.2   2021-04-18 [?] CRAN (R 4.1.0)                         
##  P xfun          0.24    2021-06-15 [?] CRAN (R 4.1.0)                         
##  P xml2          1.3.2   2020-04-23 [?] CRAN (R 4.1.0)                         
##  P yaml          2.2.1   2020-02-01 [?] CRAN (R 4.1.0)                         
## 
## [1] C:/Users/kathr/Documents/git-repos/lizard-guts-naxos/renv/library/R-4.1/i386-w64-mingw32
## [2] C:/Users/kathr/AppData/Local/Temp/RtmpKk1eNg/renv-system-library
## 
##  P -- Loaded and on-disk path mismatch.